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A modified simple RFLP-PCR method for single nucleotide polymorphism (SNP) typing Genet. Mol. Biol.
Xiao,Junhua; Xin,Xiujuan; Luan,Xiaohui; Dongzhi,Wei; Shengli,Yang.
We describe a modified single nucleotide polymorphism (SNP) typing method based on the restriction fragment length polymorphism polymerase chain reaction (RFLP-PCR). This is a simple, economical method without the need for special equipment. For most SNP loci, a common restriction endonuclease (Hind III, EcoR I or BamH I) recognizing site (RER) can be introduced into one allelic form, but not the other by two rounds of mismatched PCR. The flanking regions can be changed by as many as five bases after PCR amplification with specially designed mismatching primers so the genotypes can be distinguished after digestion of the PCR products with corresponding endonucleases.
Tipo: Info:eu-repo/semantics/article Palavras-chave: SNP genotyping; PCR-RFLP; RER site.
Ano: 2006 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572006000300028
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Cytogenetic studies in fishes of the genera Hassar, Platydoras and Opsodoras (Doradidae, Siluriformes) from Jarí and Xingú Rivers, Brazil Genet. Mol. Biol.
Milhomem,Susana Suely Rodrigues; Souza,Augusto Cesar Paes de; Nascimento,Aline Lira do; Carvalho Jr.,Jaime Ribeiro; Feldberg,Eliana; Pieczarka,Julio Cesar; Nagamachi,Cleusa Yoshiko.
We studied the karyotypes of Hassar cf. orestis and an undescribed Hassar species from the Jarí River and Opsodoras ternetzi, H. orestis and Platydoras cf. costatus from the Xingú River, all with 2n = 58. Constitutive heterochromatin is located in the centromere in most metacentric pairs; in some chromosomes this banding is not present, or it is located on the whole chromosome arm or in the distal regions. The NOR is located on a single biarmed pair at a distal region of the short arm in H. cf. orestis, H. orestis and P. cf. costatus at a distal region of the long arm in O. ternetzi and at a proximal region of the long arm in the Hassar species. In all species (except for Hassar sp.) the CMA3 analysis revealed a rich G-C region coincident with the NOR....
Tipo: Info:eu-repo/semantics/article Palavras-chave: Chromosomes; Amazon; Biodiversity; Siluriformes; Banding; Fluorochromes.
Ano: 2008 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572008000200017
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Restriction fragment analysis of the ribosomal DNA of Paratelmatobius and Scythrophrys species (Anura, Leptodactylidae) Genet. Mol. Biol.
Lourenço,Luciana B.; Garcia,Paulo C.A.; Recco-Pimentel,Shirlei M..
Physical maps of the ribosomal RNA gene 28S of species belonging to the genera Paratelmatobius and Scythrophrys were constructed, using five restriction endonucleases. The restriction sites for Bam HI, Bgl II, Bst EII, and Eco RI had similar positions in all species, although there were interspecific differences in the size of the restriction fragments obtained. An additional Pvu II site was found in Scythrophrys specimens from Piraquara (State of Paraná, Brazil) and from São Bento do Sul (State of Santa Catarina, Brazil), but not in the Scythrophrys specimens from Rancho Queimado (State of Santa Catarina, Brazil). This finding is in agreement with the hypothesis regarding the existence of two species in the genus Scythrophrys. On the other hand, the extra...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Ribosomal DNA; 28S rDNA gene; Restriction sites; Physical map; Paratelmatobius; Scythrophrys; Leptodactylidae; Anura.
Ano: 2003 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572003000200006
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Molecular cloning and functional analysis of the fatty acid-binding protein (Sp-FABP) gene in the mud crab (Scylla paramamosain) Genet. Mol. Biol.
Zeng,Xianglan; Ye,Haihui; Yang,Ya'nan; Wang,Guizhong; Huang,Huiyang.
Intracellular fatty acid-binding proteins (FABPs) are multifunctional cytosolic lipid-binding proteins found in vertebrates and invertebrates. In this work, we used RACE to obtain a full-length cDNA of Sp-FABP from the mud crab Scylla paramamosain. The open reading frame of the full length cDNA (886 bp) encoded a 136 amino acid polypeptide that showed high homology with related genes from other species. Real-time quantitative PCR identified variable levels of Sp-FABP transcripts in epidermis, eyestalk, gill, heart, hemocytes, hepatopancreas, muscle, ovary, stomach and thoracic ganglia. In ovaries, Sp-FABP expression increased gradually from stage I to stage IV of development and decreased in stage V. Sp-FABP transcripts in the hepatopancreas and hemocytes...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Fatty acid-binding protein; Immunity; Ovary development; Real-time quantitative PCR; Scylla paramamosain.
Ano: 2013 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572013000100021
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Research of the origin of a particular Tunisian group using a physical marker and Alu insertion polymorphisms Genet. Mol. Biol.
Moncer,Wifak El; Bahri,Raoudha; Esteban,Esther; Abdenni-Guenounou,Bouthaina; Moral,Pedro; Chibani,Jemni Ben; Chaabani,Hassen.
The aim of this study was to show how, in some particular circumstances, a physical marker can be used along with molecular markers in the research of an ancient people movement. A set of five Alu insertions was analysed in 42 subjects from a particular Tunisian group (El Hamma) that has, unlike most of the Tunisian population, a very dark skin, similar to that of sub-Saharans, and in 114 Tunisian subjects (Gabes sample) from the same governorate, but outside the group. Our results showed that the El Hamma group is genetically midway between sub-Saharan populations and North Africans, whereas the Gabes sample is clustered among North Africans. In addition, The A25 Alu insertion, considered characteristic to sub-Saharan Africans, was present in the El Hamma...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Tunisian population; El Hamma group; Skin color; Alu insertion polymorphisms; People movement history.
Ano: 2011 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572011000300002
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Identification of novel and conserved microRNAs in Coffea canephora and Coffea arabica Genet. Mol. Biol.
Loss-Morais,Guilherme; Ferreira,Daniela C.R.; Margis,Rogério; Alves-Ferreira,Márcio; Corrêa,Régis L..
As microRNAs (miRNAs) are important regulators of many biological processes, a series of small RNAomes from plants have been produced in the last decade. However, miRNA data from several groups of plants are still lacking, including some economically important crops. Here microRNAs from Coffea canephora leaves were profiled and 58 unique sequences belonging to 33 families were found, including two novel microRNAs that have never been described before in plants. Some of the microRNA sequences were also identified in Coffea arabica that, together with C. canephora, correspond to the two major sources of coffee production in the world. The targets of almost all miRNAs were also predicted on coffee expressed sequences. This is the first report of novel miRNAs...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Coffee; MicroRNA profiling; Illumina sequencing.
Ano: 2014 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572014000500010
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Differential gene expression and mitotic cell analysis of the drought tolerant soybean (Glycine max L. Merrill Fabales, Fabaceae) cultivar MG/BR46 (Conquista) under two water deficit induction systems Genet. Mol. Biol.
Martins,Polyana K.; Jordão,Berenice Q.; Yamanaka,Naoki; Farias,José R.B.; Beneventi,Magda A.; Binneck,Eliseu; Fuganti,Renata; Stolf,Renata; Nepomuceno,Alexandre L..
Drought cause serious yield losses in soybean (Glycine max), roots being the first plant organ to detect the water-stress signals triggering defense mechanisms. We used two drought induction systems to identify genes differentially expressed in the roots of the drought-tolerant soybean cultivar MG/BR46 (Conquista) and characterize their expression levels during water deficit. Soybean plants grown in nutrient solution hydroponically and in sand-pots were submitted to water stress and gene expression analysis was conducted using the differential display (DD) and real time polymerase chain reaction (PCR) techniques. Three differentially expressed mRNA transcripts showed homology to the Antirrhinum majus basic helix-loop-helix transcription factor bHLH, the...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Cell division; Differential display; Gene expression; Real time PCR; Soybean; Water stress.
Ano: 2008 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572008000300019
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The association of CAPN1 316 marker genotypes with growth and meat quality traits of steers finished on pasture Genet. Mol. Biol.
Miquel,María C.; Villarreal,Edgardo; Mezzadra,Carlos; Melucci,Lilia; Soria,Liliana; Corva,Pablo; Schor,Alejandro.
The objective of this paper was to determine the association of a SNP in the µ-calpain gene at position 316 with growth and quality of meat traits of steers grown on pasture. Fifty-nine Brangus and 20 Angus steers were genotyped for CAPN1 316. Warner Bratzler shear force was measured in l. lumborum samples after a 7-day aging period. A multivariate analysis of variance was performed, including shear force (WBSF), final weight (FW), average daily gain (ADG), backfat thickness (BFT), average monthly fat thickness gain (AMFTG), rib-eye area (REA), and beef rib-eye depth (RED) as dependent variables. The CAPN1 316 genotype was statistically significant. Univariate analyses were done with these variables. The marker genotype was statistically significant (p...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Beef cattle; Tenderness; Growth; Molecular marker; Multivariate analysis.
Ano: 2009 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572009000300011
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Genetic characterization of 18 novel microsatellite loci in northern pike (Esox lucius L.) Genet. Mol. Biol.
Wang,Jun; Wang,Chenghui; Qian,Long; Ma,Yuqing; Yang,Xinxin; Jeney,Zsigmond; Li,Sifa.
The northern pike (Esox lucius L.), an important predatory freshwater species, is undergoing significant population decline. In this study, 18 novel polymorphic microsatellite loci were isolated and used for assessing genetic variation in the Chinese Ulungur and Hungarian Balaton populations of the species. The number of alleles ranged from 2 to 13, observed heterozygosity from 0.154 to 0.920 and expected heterozygosity from 0.145 to 0.921, thereby indicating the specific usefulness of these suites of markers for investigating genetic variability.
Tipo: Info:eu-repo/semantics/article Palavras-chave: Northern pike; Microsatellite loci; Genetic variability.
Ano: 2011 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572011000100029
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The parametric restrictions of the Griffing diallel analysis model: combining ability analysis Genet. Mol. Biol.
Viana,José Marcelo Soriano.
It was studied the parametric restrictions of the diallel analysis model of Griffing, method 2 (parents and F1 generations) and model 1 (fixed), in order to address the questions: i) does the statistical model need to be restricted? ii) do the restrictions satisfy the genetic parameter values? and iii) do they make the analysis and interpretation easier? Objectively, these questions can be answered as: i) yes, ii) not all of them, and iii) the analysis is easier, but the interpretation is the same as in the model with restrictions that satisfy the parameter values. The main conclusions were that: the statistical models for combining ability analysis are necessarily restricted; in the Griffing model (method 2, model 1), the restrictions relative to the...
Tipo: Info:eu-repo/semantics/article
Ano: 2000 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572000000400029
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Evaluation of noise reduction techniques in the splice junction recognition problem Genet. Mol. Biol.
Lorena,Ana C.; Carvalho,André C. P. L. F. de.
The Human Genome Project has generated a large amount of sequence data. A number of works are currently concerned with analyzing these data. One of the analyses carried out is the identification of genes' structures on the sequences obtained. As such, one can search for particular signals associated with gene expression. Splice junctions represent a type of signal present on eukaryote genes. Many studies have applied Machine Learning techniques in the recognition of such regions. However, most of the genetic databases are characterized by the presence of noisy data, which can affect the performance of the learning techniques. This paper evaluates the effectiveness of five data pre-processing algorithms in the elimination of noisy instances from two splice...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Pre-processing; Machine learning; Splice junction recognition.
Ano: 2004 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572004000400031
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Karyotypic description of four species of Trigona (Jurine, 1807) (Hymenoptera, Apidae, Meliponini) from the State of Mato Grosso, Brazil Genet. Mol. Biol.
Costa,Kleber França; Brito,Rute Magalhães; Miyazawa,Carlos Suetoshi.
The genus Trigona contains at least 31 species, but there have been few cytogenetic studies of this group. In this work, four species of Trigona (T. branneri, T. chanchamayoensis, T. hyalinata, and T. recursa) from the municipality of Cuiabá, in the State of Mato Grosso, Brazil, were studied. In all of the species, the females had 2n = 34 chromosomes and the males had n = 17. The C-banding patterns showed that the karyotypes of these species consisted mainly of acrocentric and pseudoacrocentric chromosomes. These cytogenetic findings should useful in future phylogenetic studies of this group.
Tipo: Info:eu-repo/semantics/article Palavras-chave: Cytogenetics; Karyotype; Meliponini; Stingless bees; Trigona.
Ano: 2004 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572004000200010
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Karyotypic characterization of Hydromedusa tectifera (Testudines, Pleurodira) from the upper Iguaçu River in the Brazilian state of Paraná Genet. Mol. Biol.
Noleto,Rafael Bueno; Kantek,Daniel Luis Zanella; Swarça,Ana Cláudia; Dias,Ana Lúcia; Fenocchio,Alberto Sergio; Cestari,Marta Margarete.
We present the karyotypic characterization of 26 specimens of the side-necked turtle Hydromedusa tectifera collected in the upper Iguaçu River, Paraná state, Brazil. The turtles were cytogenetically analyzed using Giemsa staining and other banding techniques (C, G, Ag-NOR and CMA3) as well as fluorescence in situ hybridization (FISH) with a rDNA 18S probe. All the specimens showed a diploid number of 58 composed of 22 macro and 36 microchromosomes. The Ag-NOR, CMA3 and FISH techniques permitted the identification and characterization of the chromosome pairs bearing nucleolus organizer regions (NORs), while G-banding facilitated a better recognition and pairing of macrochromosomes. These data agree with some information available in the literature and...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Chromosomes; FISH; G-banding; Pleurodira; Turtle.
Ano: 2006 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572006000200011
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Association between G316A growth hormone polymorphism and economic traits in pigs Genet. Mol. Biol.
Faria,Danielle Assis de; Guimarães,Simone Eliza Facioni; Lopes,Paulo Sávio; Pires,Aldrin Vieira; Paiva,Samuel Rezende; Sollero,Bruna Pena; Wenceslau,Amauri Arias.
The association between G316A growth hormone polymorphism and quantitative traits was investigated in an F2 population of pigs. Association analyses were performed using a statistical model that included genotype, sex, batch and sex by genotype interaction as fixed effects and sire as random effect. The polymorphism was associated with the number of right teats (p = 0.03), heart weight (p = 0.04), lung weight (p = 0.05), carcass length determined by the Brazilian carcass classification method (p = 0.04), picnic shoulder weight (p = 0.07), jowl weight (p = 0.01), pH 24 h after slaughtering (p = 0.03) and drip loss (p = 0.01). Interaction between genotype and sex was observed for six performance traits. The additive effect was significant (p < 0.10) for...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Candidate genes; Divergent cross; Molecular marker; Sex x genotype interaction; Swine.
Ano: 2006 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572006000400010
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A note on the population genetic consequences of delayed larval development in insects Genet. Mol. Biol.
Salles,Marcos Mattoso de; Otto,Paulo A..
Observations by Dobzhansky's group in the 1940s suggesting that the presence of recessive genotypes could account for lower larval developmental rates in Drosophila melanogaster were not confirmed at the time and all subsequent investigations on this subject focused on the analysis of ecological models based on competition among pre-adult individuals. However, a paper published in this journal in 1991 eventually confirmed the finding made by Dobzhansky and his co-workers. In this report, we provide a theoretical analysis of the population genetic effects of a delay in the rate of larval development produced by such a genetic mechanism.
Tipo: Info:eu-repo/semantics/article Palavras-chave: Difference and differential equations; Drosophila; Dynamic systems; Larval development; Population genetics.
Ano: 2013 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572013000300019
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Chromosomal locations of the maize (Zea mays L.) HtP and rt genes that confer resistance to Exserohilum turcicum Genet. Mol. Biol.
Ogliari,Juliana Bernardi; Guimarães,Marco Antônio; Camargo,Luis Eduardo Aranha.
We used 125 microsatellite markers to genotype the maize (Zea mays L.) near isogenic lines (NIL) L30HtPHtPRtRt and L30htphtpRtRt and the L40htphtprtrt line which contrast regarding the presence of the recently described dominant HtP and the recessive rt genes that confer resistance to Exserohilum turcicum. Five microsatellite markers revealed polymorphisms between the NIL and were considered candidate linked markers for the HtP resistance gene. Linkage was confirmed by bulked segregant sample (BSS) analysis of 32 susceptible and 34 resistant plants from a BC1F1 population derived from the cross (L30HtPHtPRtRt x L40htphtprtrt) x L40htphtprtrt. The bnlg198 and dupssr25 markers, both located on maize chromosome 2L (bin 2.08), were polymorphic between bulks....
Tipo: Info:eu-repo/semantics/other Palavras-chave: Bulked segregant sample analysis; Microsatellite markers; Maize; Near-isogenic lines; Northern leaf blight.
Ano: 2007 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572007000400021
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Genetic analysis of adult-plant resistance to leaf rust in a double haploid wheat (Triticum aestivum L. em Thell) population Genet. Mol. Biol.
Brammer,Sandra Patussi; Fernandes,Maria Irene Baggio de Moraes; Barcellos,Amarilis Labes; Milach,Sandra Cristina Kothe.
A genetic analysis of adult plant resistance to leaf rust (Puccinia triticina) was performed in in vitro obtained double haploid progenies from a cross between the Brazilian wheat cultivar Trigo BR 35, which, under the high inoculum pressure of the southern region, has been resistant to leaf rust for more than 12 years, and the susceptible cultivar IAC 13-Lorena. Haplodiploidization via in vitro gimnogenesis was done by somatic elimination of the pollen donor genome after maize pollination of the F1 plants. The advantages and usefulness of double haploids (DH) for genetic analysis of complex inherited traits like durable adult-plant resistance to wheat leaf rust were evident: it was possible to analyze inheritance patterns in this cross by using only the...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Puccinia triticina; Resistant genes; Haplodiploidization.
Ano: 2004 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572004000300020
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-866G/A and Ins/Del polymorphisms in the UCP2 gene and diabetic kidney disease: case-control study and meta-analysis Genet. Mol. Biol.
Dieter,Cristine; Assmann,Taís Silveira; Lemos,Natália Emerim; Massignam,Eloísa Toscan; Souza,Bianca Marmontel de; Bauer,Andrea Carla; Crispim,Daisy.
Abstract Uncoupling protein 2 (UCP2) decreases reactive oxygen species (ROS). ROS overproduction is a key contributor to the pathogenesis of diabetic kidney disease (DKD). Thus, UCP2 polymorphisms are candidate risk factors for DKD; however, their associations with this complication are still inconclusive. Here, we describe a case-control study and a meta-analysis conducted to investigate the association between UCP2 -866G/A and Ins/Del polymorphisms and DKD. The case-control study comprised 385 patients with type 1 diabetes mellitus (T1DM): 223 patients without DKD and 162 with DKD. UCP2 -866G/A (rs659366) and Ins/Del polymorphisms were genotyped by real-time PCR and conventional PCR, respectively. For the meta-analysis, a literature search was conducted...
Tipo: Info:eu-repo/semantics/article Palavras-chave: UCP2; Polymorphisms; Diabetic kidney disease.
Ano: 2020 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572020000400101
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Method optimization for proteomic analysis of soybean leaf: improvements in identification of new and low-abundance proteins Genet. Mol. Biol.
Mesquita,Rosilene Oliveira; Soares,Eduardo de Almeida; Barros,Everaldo Gonçalves de; Loureiro,Marcelo Ehlers.
The most critical step in any proteomic study is protein extraction and sample preparation. Better solubilization increases the separation and resolution of gels, allowing identification of a higher number of proteins and more accurate quantitation of differences in gene expression. Despite the existence of published results for the optimization of proteomic analyses of soybean seeds, no comparable data are available for proteomic studies of soybean leaf tissue. In this work we have tested the effects of modification of a TCA-acetone method on the resolution of 2-DE gels of leaves and roots of soybean. Better focusing was obtained when both mercaptoethanol and dithiothreitol were used in the extraction buffer simultaneously. Increasing the number of washes...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Proteomics; Glycine max; 2-DE; Protein extraction; Leaf proteome.
Ano: 2012 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572012000200017
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An effective homologous cloning method for isolating novel miR172s from Phalaenopsis hybrida Genet. Mol. Biol.
Han,Ying Ying; Yan,Qin Hua; Ming,Feng.
MiR172 is an important microRNA that regulates floral development in various plants and downregulates AP2 family members to relieve the stress on floral determinacy, leading to phase transition from vegetative to reproductive growth. In this work, PCR with primers designed based on the rice miR172 sequence was used to isolate two miR172-like transcripts from Phalaenopsis hybrida (PhmiR172-1 and PhmiR172-2) that were very similar to Oryza miR172d and Arabidopsis miR172b. RT-PCR indicated that the levels of these two transcripts were negatively correlated with the level of the Phalaenopsis AP2 (PhAP2) gene in stem, root, pedicel and sepal, and that both were co-expressed with PhAP2 in young buds. Overproduction of PhmiR172-2 in Arabidopsis led to early...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Homologous cloning; MiR172; MiRNA; Phalaenopsis; Sequence conservation.
Ano: 2014 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572014000300014
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